DAVID Bioinformatics 6.7
The Database for Annotation, Visualization and Integrated Discovery
DAVID Bioinformatics Resources 6.7
National Institute of Allergy and Infectious Diseases (NIAID), NIH
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web service

DAVID Web Service

Comments and Suggestions!

DAVID web service allows users to programmatically (Java, Perl, Python, etc) interact with the DAVID to automate user tasks. It is an enhancement and extension of current url-based DAVID API with more control and less limitations for users. To begin to use please register and download the client code. For license information, check our license page.

 

Service EPR : http://david-d.ncifcrf.gov/webservice/services/DAVIDWebService

 

Available Operations & WSDL:

  • authenticate(authenticate user by email address; return true if user has registered email with DAVID knowledge base)
  • addList (add a gene list or background list to current session; arguments include inputIds, idType, listName, listType)
  • getAllAnnotationCategoryNames (return all available annotation category names; no argument needed)
  • getAllListNames (return all list names; no argument needed)
  • getAllPopulationNames (return background names; no argument needed)
  • getChartReport (generate chart report; arguments include threshold, count)
  • getConversionTypes (return all acceptable idTypes; no argument needed)
  • getCurrentList (return the position of current list; no argument needed)
  • getCurrentSpecies (return current species of the current list; no argument needed)
  • getCurrentPopulation (return the position of current background list; no argument needed)
  • getDefaultCategoryNames (return all default category names; no argument needed)
  • getGeneClusterReport (generate gene cluster report; arguments include overlap, initialSeed, finalSeed, linkage, kappa)
  • getGeneReportCategories(return gene report categories; no argument needed)
  • getListName (get the name of a list; argument is the position of the list)
  • getListReport (generate list report; no argument needed)
  • getSpecies (return species of the current list; no argument needed)
  • getSummaryReport (return a summary report; no argument needed)
  • getTableReport (generate table report; no argument needed)
  • getTermClusterReport (generate term cluster report; arguments include overlap, initialSeed, finalSeed, linkage, kappa)
  • setCurrentList (switch between gene lists; argument is the position of the list)
  • setCurrentPopulation (switch between background lists; argument is the position of the list)
  • setCurrentSpecies (select specie(s) to use; argument is a string of integers delimited by commas)
  • setCategories (let user select categories; argument is a string with category names delimited by commas; return a list of validated category names)
  • loadTesting (used by DAVID team; arguments include userName, reportTypes, listName, listType, idType, inputIds)

Some Limitations:

  • A job with more than 3000 genes to generate gene or term cluster report will not be handled by DAVID due to resource limit.
  • No more than 200 jobs in a day from one user or computer.
  • DAVID Team reserves right to suspend any improper uses of the web service without notice.

 

Download client code:

JavaClient-1.1.zip (README.txt)

PerlClient-1.1.zip (README.txt)

PythonClient-1.1.zip (README.txt)

Matlab-1.1.zip (note1 and note2)

R package (a note )

 

To cite our work:

Xiaoli Jiao, Brad T. Sherman, Da Wei Huang, Robert Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki

DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis Bioinformatics bts251 2012 doi:10.1093/bioinformatics/bts251

 

Join the forum: http://david-d.ncifcrf.gov/forum/viewforum.php?f=14

 

 

 

 




 Please cite Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 within any publication that makes use of any methods inspired by DAVID.
                          

        

                 
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